Porphyromonas gingivalis (DSM 28984, HG66)

Name: Porphyromonas gingivalis (DSM 28984, HG66)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24337

Type strain

Strain Designation HG66

Culture col. no. DSM 28984 HG66

NCBI tax ID(s) 837

Special Collections DSMZ

History <- J. Potempa <- R. Arnold, Emory University; HG66

Links

Porphyromonas gingivalis HG66 is an anaerobe, mesophilic human pathogen that was isolated from human oral cavity.

anaerobe mesophilic human pathogen genome sequence

Name and taxonomic classification

SI-ID 407947

DSM 28984

@ref 20215

Last LPSN update 2026-02-09 11:23:57

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Porphyromonadaceae

Genus Porphyromonas

Species Porphyromonas gingivalis

Full scientific name Porphyromonas gingivalis (Coykendall et al. 1980) Shah and Collins 1988

Synonyms (1)

Bacteroides gingivalis

BacDive ID	Other strains from **Porphyromonas gingivalis** (8)	Type strain
12506	P. gingivalis 2561, DSM 20709, ATCC 33277, CIP 103683, ... (type strain)
144481	P. gingivalis CCUG 25211
144483	P. gingivalis CCUG 25226
144589	P. gingivalis CCUG 25839
144832	P. gingivalis CCUG 26712
145130	P. gingivalis CCUG 27724
162568	P. gingivalis JCM 19600
165806	P. gingivalis JCM 8525

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.437
125439	negative	98.4

Colony morphology

20739

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20739	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
20739	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20739	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

20739

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.996
125439		98.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	+	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
20739	-	-	-	+/-	-	-	-	-	-	+	-	-	-	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
20739	-	-	-	+	+/-	-	-	-	-	+	-	-	-	-	-	+	+	-	-	+	-	-	+/-	-	+	-	-	+/-	-
20739	-	+	-	+	+/-	-	-	-	-	+	-	-	-	-	-	+	+	-	-	+	-	-	+/-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	-
#Host Body-Site	#Oral cavity and airways	#Mouth

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
20739	human oral cavity	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
20739			2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM73941v1 assembly for Porphyromonas gingivalis HG66	chromosome	GCA_000739415	837.47	2597490155	837	88.27

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Porphyromonas gingivalis HG66
IMG: 2597490155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	61.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	65.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Porphyromonas gingivalis HG66
NCBI: GCA_000739415.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.44	no
125438	anaerobic	anaerobicⓘ	yes	85.23	no
125438	aerobic	aerobicⓘ	no	91.44	yes
125438	spore-forming	spore-formingⓘ	no	94.00	no
125438	thermophilic	thermophileⓘ	no	93.74	yes
125438	flagellated	motile2+ⓘ	no	87.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification of anaerobic bacterial strains by pyrolysis-gas chromatography-ion mobility spectrometry.	Kobelt T, Klose J, Mukherjee R, Lippmann M, Szafranski SP, Stiesch M, Zimmermann S.	Front Bioeng Biotechnol	10.3389/fbioe.2025.1582565	2025
	Laser-assisted microbial culturomics.	Qu T, Koch L, Mukherjee R, Tu Y, Seidel AL, Puttmann LD, Winkel A, Yang I, Grischke J, Liu D, Wolkers WF, Kittler S, Chichkov B, Stiesch M, Szafranski SP.	Nat Commun	10.1038/s41467-025-66804-7	2025
Genetics	In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics.	Chen T, Siddiqui H, Olsen I.	Front Cell Infect Microbiol	10.3389/fcimb.2017.00028	2017
Genetics	Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984).	Siddiqui H, Yoder-Himes DR, Mizgalska D, Nguyen KA, Potempa J, Olsen I	Genome Announc	10.1128/genomeA.00947-14	2014

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20739	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28984
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#68380	Automatically annotated from API rID32A .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Porphyromonas gingivalis (DSM 28984, HG66)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000739415

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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